Magnesium in PDB 6xrc: Apo Nis Synthetase Desd Variant R306Q

The structure of Apo Nis Synthetase Desd Variant R306Q, PDB code: 6xrc was solved by K.M.Hoffmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.47 / 2.45
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.417, 98.921, 183.352, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 27

The binding sites of Magnesium atom in the Apo Nis Synthetase Desd Variant R306Q (pdb code 6xrc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Apo Nis Synthetase Desd Variant R306Q, PDB code: 6xrc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Apo Nis Synthetase Desd Variant R306Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apo Nis Synthetase Desd Variant R306Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:57.2 occ:1.00 OE2 A:GLU445 2.2 45.3 1.0 O2A A:ATP703 2.4 56.1 1.0 OD1 A:ASN446 2.5 30.7 1.0 H5'2 A:ATP703 2.6 49.9 1.0 HB3 A:GLU445 2.6 34.1 1.0 HE1 A:HIS443 2.7 29.8 1.0 O3B A:ATP703 2.9 85.5 1.0 O3A A:ATP703 2.9 61.2 1.0 O3G A:ATP703 2.9 94.4 1.0 PA A:ATP703 3.1 58.8 1.0 OD2 A:ASP463 3.2 49.8 1.0 CD A:GLU445 3.2 39.9 1.0 CG A:ASN446 3.4 30.3 1.0 CB A:GLU445 3.4 34.0 1.0 C5' A:ATP703 3.4 49.9 1.0 PG A:ATP703 3.6 0.0 1.0 CG A:GLU445 3.6 37.8 1.0 HG3 A:GLU445 3.6 37.8 1.0 CE1 A:HIS443 3.6 29.9 1.0 PB A:ATP703 3.6 67.7 1.0 O5' A:ATP703 3.7 56.0 1.0 ND2 A:ASN446 3.7 30.2 1.0 HZ1 A:LYS462 3.9 40.9 1.0 HZ2 A:LYS462 4.0 40.7 1.0 HB2 A:GLU445 4.0 34.0 1.0 HB2 A:SER278 4.0 30.3 1.0 CG A:ASP463 4.1 50.6 1.0 H5'1 A:ATP703 4.1 49.9 1.0 H4' A:ATP703 4.1 47.9 1.0 HB2 A:ASP463 4.1 45.1 1.0 HA A:ASN446 4.2 29.4 1.0 C A:GLU445 4.2 30.6 1.0 NE2 A:HIS443 4.3 30.6 1.0 C4' A:ATP703 4.3 47.9 1.0 O1B A:ATP703 4.3 68.0 1.0 OE1 A:GLU445 4.4 40.3 1.0 N A:ASN446 4.4 29.3 1.0 NZ A:LYS462 4.4 40.9 1.0 HB3 A:SER278 4.4 30.3 1.0 O A:GLU445 4.4 29.3 1.0 CA A:GLU445 4.5 32.2 1.0 O1G A:ATP703 4.5 1.0 1.0 O4' A:ATP703 4.5 47.6 1.0 O1A A:ATP703 4.5 60.5 1.0 HG2 A:GLU445 4.5 37.8 1.0 CB A:ASP463 4.6 45.4 1.0 CB A:ASN446 4.6 30.3 1.0 CA A:ASN446 4.6 29.4 1.0 ND1 A:HIS443 4.7 29.5 1.0 CB A:SER278 4.7 30.3 1.0 O2G A:ATP703 4.7 97.6 1.0 O2B A:ATP703 4.7 65.2 1.0 H A:ASN446 4.8 29.3 1.0 HB3 A:ASP463 4.8 45.5 1.0 HZ3 A:LYS462 4.8 41.0 1.0 HB2 A:ASN446 5.0 30.3 1.0

Magnesium binding site 2 out of 3 in the Apo Nis Synthetase Desd Variant R306Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Apo Nis Synthetase Desd Variant R306Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:46.5 occ:1.00 O2G B:ATP702 2.3 80.4 1.0 O2A B:ATP702 2.3 57.0 1.0 OD1 B:ASN446 2.3 25.4 1.0 HG3 B:GLU445 2.5 37.7 1.0 OE2 B:GLU445 2.7 41.5 1.0 O3B B:ATP702 2.8 77.2 1.0 O3A B:ATP702 3.0 59.5 1.0 PG B:ATP702 3.1 96.2 1.0 CG B:GLU445 3.2 37.7 1.0 PA B:ATP702 3.2 58.0 1.0 OD2 B:ASP463 3.2 48.3 1.0 CG B:ASN446 3.3 26.5 1.0 CD B:GLU445 3.4 41.4 1.0 HG2 B:GLU445 3.4 37.7 1.0 H5'2 B:ATP702 3.4 54.2 1.0 HB2 B:ASP463 3.4 41.2 1.0 HZ1 B:LYS462 3.4 43.0 1.0 HZ2 B:LYS462 3.6 42.8 1.0 PB B:ATP702 3.6 61.4 1.0 ND2 B:ASN446 3.7 26.4 1.0 CG B:ASP463 3.7 46.0 1.0 NZ B:LYS462 3.9 42.9 1.0 HA B:ASN446 3.9 27.0 1.0 NE2 B:HIS443 4.0 27.9 1.0 CB B:ASP463 4.0 41.5 1.0 O3G B:ATP702 4.0 89.4 1.0 HZ3 B:LYS462 4.1 43.0 1.0 HB2 B:SER278 4.1 31.7 1.0 O1B B:ATP702 4.1 58.0 1.0 HB3 B:ASP463 4.2 41.6 1.0 C5' B:ATP702 4.2 54.2 1.0 O5' B:ATP702 4.2 54.2 1.0 O1G B:ATP702 4.2 76.4 1.0 O1A B:ATP702 4.3 60.9 1.0 C B:GLU445 4.4 29.1 1.0 O B:GLU445 4.4 28.9 1.0 HB3 B:SER278 4.5 31.7 1.0 CB B:GLU445 4.5 33.6 1.0 CB B:ASN446 4.5 27.1 1.0 CA B:ASN446 4.5 27.0 1.0 N B:ASN446 4.6 27.3 1.0 OE1 B:GLU445 4.6 49.1 1.0 H4' B:ATP702 4.6 52.2 1.0 HE1 B:HIS443 4.7 28.4 1.0 OD1 B:ASP463 4.7 52.6 1.0 HB3 B:GLU445 4.7 33.7 1.0 CE1 B:HIS443 4.7 28.3 1.0 CB B:SER278 4.8 31.8 1.0 O2B B:ATP702 4.8 62.5 1.0 HG3 B:LYS462 4.8 37.0 1.0 C4' B:ATP702 4.9 52.2 1.0 H5'1 B:ATP702 4.9 54.2 1.0 HB2 B:ASN446 4.9 27.1 1.0 CD2 B:HIS443 5.0 27.8 1.0

Magnesium binding site 3 out of 3 in the Apo Nis Synthetase Desd Variant R306Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Apo Nis Synthetase Desd Variant R306Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:55.7 occ:1.00 O1A B:ATP702 2.3 60.9 1.0 O1B B:ATP702 2.6 58.0 1.0 OE2 B:GLU467 2.8 54.9 1.0 OD2 B:ASP463 3.6 48.3 1.0 PA B:ATP702 3.7 58.0 1.0 CD B:GLU467 3.8 50.5 1.0 PB B:ATP702 3.9 61.4 1.0 HB2 B:GLU466 3.9 55.4 1.0 OE1 B:GLU466 4.0 65.2 1.0 HZ2 B:LYS294 4.0 33.2 1.0 O3A B:ATP702 4.0 59.5 1.0 HB3 B:GLU466 4.1 55.9 1.0 HH21 B:ARG280 4.1 38.9 1.0 HG2 B:GLU467 4.3 48.6 1.0 CB B:GLU466 4.4 55.8 1.0 O2A B:ATP702 4.4 57.0 1.0 OE1 B:GLU467 4.5 51.1 1.0 CG B:ASP463 4.5 46.0 1.0 OD1 B:ASP463 4.6 52.6 1.0 HH22 B:ARG280 4.7 39.4 1.0 CG B:GLU467 4.7 48.5 1.0 NH2 B:ARG280 4.7 39.1 1.0 CD B:GLU466 4.7 66.0 1.0 O2B B:ATP702 4.8 62.5 1.0 O5' B:ATP702 4.8 54.2 1.0 NZ B:LYS294 4.9 33.3 1.0 HG3 B:GLU467 4.9 48.2 1.0 HG3 B:GLU466 5.0 61.5 1.0 CG B:GLU466 5.0 61.8 1.0

K.M.Hoffmann, E.S.Goncuian, K.L.Karimi, C.R.Amendola, Y.Mojab, K.M.Wood, G.A.Prussia, J.Nix, M.Yamamoto, K.Lathan, I.W.Orion. Cofactor Complexes of Desd, A Model Enzyme in the Virulence-Related Nis Synthetase Family. Biochemistry V. 59 3427 2020.
ISSN: ISSN 0006-2960
PubMed: 32885650
DOI: 10.1021/ACS.BIOCHEM.9B00899